Methods for cancer treatment using tak1 inhibitors

ABSTRACT

The invention includes, in part, a method of inhibiting lymphoid tumour cell proliferation by contacting the lymphoid with a TAK1 inhibitor.

FIELD OF THE INVENTION

The present invention relates to the treatment of cancer.

BACKGROUND OF THE INVENTION

Lymphoid (B-cell and T-cell) tumours account for a significantproportion of human malignancies. The spectrum of different, butrelated, B cell malignancies includes B-cell acute lymphocytic leukemia(B-ALL), B-cell chronic lymphocytic leukemia (B-CLL), B-cell chronicmyelogenous leukemia (B-CML), B-cell prolymphocytic leukemia (B-PLL),hairy cell leukemia (HCL), various B-cell non-Hodgkin's lymphomas(B-NHLs) (including diffuse large B cell lymphoma (DLBCL), FollicularLymphoma (FCL or FL), mantle cell lymphoma (MCL), marginal zone lymphoma(MZL), Primary effusion lymphoma (PEL)) and Multiple Myeloma (MM). Thespectrum of T-cell malignancies includes T-cell leukaemia, peripheralT-cell lymphoma (PTCL), T-cell lymphoblastic lymphoma (T-CLL), cutaneousT-cell lymphoma (CTCL) and adult T-cell lymphoma (ATCL). Treatment ofnon-Hodgkin's lymphomas including both B-cell and T-cell tumours,chronic lymphocytic leukemias (CLL) and multiple myelomas (MM) isfrequently unsatisfactory and attempts to link clinical or cellularcharacteristics of the disease to prognosis and treatment have met withdifficulties.

SUMMARY OF THE INVENTION

The present invention is based, in part, on methods that can be used totreat a patient having cancer with a TGF-beta activated kinase 1 (TAK1,MAP3K7) inhibitor. The invention further includes selecting patientshaving cancer who would be responsive to treatment with a TAK1inhibitor. Moreover, the invention includes methods for determining forthe presence of one or more deregulated TAK1 signal transductionmolecules in a tumour cell. The presence of a deregulated TAK1 signaltransduction molecule indicates that a TAK1 inhibitor should beadministered.

In one aspect, the invention includes inhibiting B cell tumour cellproliferation by contacting a B cell tumour cell with a TAK1 inhibitor.The B cell tumour can be a non-Hodgkin's lymphoma, a chronic lymphocyticleukaemia, or a multiple myeloma.

In another aspect, the invention includes inhibiting the growth of asolid tumour by contacting the tumour with a TAK1 inhibitor. The solidtumour can be a tumour of the head and neck, breast, ovary, lung,pancreas, colon, prostate, liver, kidney or skin.

In another aspect, the invention includes inhibiting proliferation of aT-cell leukemia and T-cell lymphoma by contacting the T-cell leukaemiaand T-cell lymphoma with a TAK1 inhibitor. A T cell leukemia can includeT-cell acute lymphoblastic leukemia (T-ALL), T-lymphoblastic lymphoma,T-CLL, CTCL or other T-NHLs. The TAK1 inhibitor can be administeredeither as a single agent or in combination with other anti-cancer agentsor anti-cancer antibodies.

In another aspect, the invention includes a method of treating cancer.In one aspect, the invention includes a method of treating a patienthaving a B cell tumour by administering a TAK1 inhibitor. The B-celltumour can be a non-Hodgkin's lymphoma, a chronic lymphocytic leukaemiaor a multiple myeloma. In one example, the non-Hodgkin's lymphoma can bea follicular lymphoma, a diffuse large B cell lymphoma (DLBCL) ofactivated B cell (ABC) type, a diffuse large B cell lymphoma (DLBCL) ofgerminal center B cell (GCB) type, a mantle zone lymphoma (MZL), Mantlecell lymphoma (MCL), or MALT Lymphoma.

In another example, the non-Hodgkin's lymphoma has a t(14;18)(q32;q21)translocation, t(11;18)(q21;q21) translocation, t(1;14)(p22;q32),amplification of chromosome 18, addition of chromosome 18q21,amplification of chromosome 6, or amplification, as defined bycomparative genomic hybridisation, of specific regions including BCL-10,CARD11, TRAF6 and TAK1.

In another aspect, the invention includes treating a patient having asolid tumour by administering a TAK1 inhibitor. The solid tumour can bea tumour of the head and neck, breast, ovary, lung, pancreas, colon,prostate, or skin.

In another aspect, the invention includes treating a patient having aT-cell leukemia by contacting the T-cell leukemia with a TAK1 inhibitor.A T-cell leukemia can include T-cell acute lymphoblastic leukemia(T-ALL), T-lymphoblastic lymphoma, T-CLL, CTCL or other T-NHLs.

In yet another aspect, the invention includes a method of treating apatient having a deregulated TAK1 signalling transduction molecule byadministering a TAK1 inhibitor. The TAK1 signalling transductionmolecule can be MALT1, BCL-10, TAB1, TAB2, TRAF6, TRAF2, TAK1, CARD11,IRAK1, IRAK4, API1, API2, API3, API4 (survivin), BCL2 or NFkB targetgenes. The TAK1 signalling molecule can be a DNA molecule in eithermutated or amplified or translocated form. The TAK1 signaling moleculecan be a protein in its naïve form or modified, either byphosphorylation, ubiquitination, changed in sequence due to mutation,etc. The TAK1 signaling molecule can also be monitored by itssubcellular localization. One example of such alterations in subcellularlocalization is shown by increased nuclear localization of BCL10 due tothe gene amplification in a diffuse large B cell lymphoma with IGH-BCL2fusion (Ye H et. al Haematologica. 2006; 91 (6 Suppl)).

In another embodiment, a deregulated TAK1 signalling transductionmolecule can be one or more of the molecules listed in Table 1 or Table2 below.

TABLE 1 Gene Symbol Entrez Pathway U133A/B RANK 8792 Rank-L 207037_at;238846_at; RANKL 8600 Rank-L 210643_at; 211153_s_at; 241248_at; TNFR17132 TNF 207643_s_at; 241944_x_at; TNFR2 7133 TNF 203508_at; TRADD 8717TNF 1729_at; 205641_s_at; 213443_at; TANK 10010 TNF 207616_s_at;209451_at; 210458_s_at; 241191_at; 243376_at; GCK 2645 TNF 211167_s_at;RIP 3267 TNF 213926_s_at; 213928_s_at; RAIDD 8738 TNF 209833_at;242638_at; PROCASP2 835 TNF 208050_s_at; 209811_at; 209812_x_at;211140_s_at; 34449_at; 226032_at; 226036_x_at; UBC13 7334 TNF201523_x_at; 201524_x_at; 212751_at; UEV1A 7335 TNF 240129_at; TLR2 7097TLRs 204924_at; TLR4 7099 TLRs 221060_s_at; 224341_x_at; 232068_s_at;240948_at; TLR3 7098 TLRs 206271_at; TLR7 51284 TLRs 220146_at;222952_s_at; TLR9 54106 TLRs 223903_at; TLR10 81793 TLRs 223750_s_at;223751_x_at; MYD88 4615 TLRs 209124_at; TOLLIP 54472 TLRs 217930_s_at;222469_s_at; 233881_s_at; IRAK 3654 TLRs 201587_s_at; TIRAP 114609 TLRs236687_at; 239796_x_at; PKR 5610 TLRs 204211_x_at; TBK1 29110 TLRs218520_at; TGFB 7040 TGF-beta 203084_at; 203085_s_at; IL1R 3554 IL1202948_at; 215561_s_at; TOLLIP 54472 IL1 217930_s_at; 222469_s_at;233881_s_at; MYD88 4615 IL1 209124_at; CD19 930 B-Cell 206398_s_at; CD22933 B-Cell CD45 5788 B-Cell 207238_s_at; 212587_s_at; 212588_at; CD79A973 B-Cell 205049_s_at; CD79B 974 B-Cell 205297_s_at; LYN 4067 B-Cell202625_at; 202626_s_at; 210754_s_at; 239555_at; 243633_at; SHP1 8431B-Cell 206410_at; SYK 6850 B-Cell 207540_s_at; 209269_s_at; 226068_at;244023_at; GAB1 2549 B-Cell 207112_s_at; 225998_at; 242572_at; GAB2 9846B-Cell 203853_s_at; 238403_at; 238405_at; 241004_at; SHP2 5781 B-Cell205867_at; 205868_s_at; 209895_at; 209896_s_at; 212610_at; CSK 1445B-Cell 202329_at; PAG 55824 B-Cell 225622_at; 225626_at; VAV 7409 B-Cell206219_s_at; VAV2 7410 B-Cell 205536_at; 205537_s_at; 226063_at; GRB22885 B-Cell 215075_s_at; 223049_at; 228572_at; BLNK 29760 B-Cell207655_s_at; 244172_at; SOS 6654 B-Cell 212777_at; 212780_at; 229261_at;230337_at; 232883_at; 242018_at; 242682_at; PLCG2 5336 B-Cell 204613_at;PKCB 5579 B-Cell 207957_s_at; 209685_s_at; 227817_at; 227824_at;228795_at; 230437_s_at; PRKCQ 5588 B-Cell 210038_at; 210039_s_at; PRKCQ5588 T-Cell 210038_at; 210039_s_at; PKCB 5579 T-Cell 207957_s_at;209685_s_at; 227817_at; 227824_at; 228795_at; 230437_s_at; CD28 940T-Cell 206545_at; 211856_x_at; 211861_x_at; CD3 917 T-Cell 206804_at;CD3E 916 T-Cell 205456_at; CD3D 915 T-Cell 213539_at; CD4 920 T-Cell203547_at; 216424_at; UBC4 7322 T-Cell 201343_at; 201344_at;201345_s_at; 215604_x_at; 240139_at; UBC5 6923 T-Cell 200085_s_at;213877_x_at; 200085_s_at; CIAP1 329 T-Cell 202076_at; CIAP2 330 T-Cell210538_s_at; 230499_at; CD8 925 T-Cell 205758_at; CD8B 926 T-Cell207979_s_at; 215332_s_at; 230037_at; CD45 5788 T-Cell 207238_s_at;212587_s_at; 212588_at; ZAP70 7535 T-Cell 214032_at; FYN 2534 T-Cell210105_s_at; 212486_s_at; 216033_s_at; 217697_at; 243006_at; CLTA4 1493T-Cell 221331_x_at; 231794_at; 234362_s_at; 234895_at; 236341_at; PI3k5286 T-Cell 213070_at; 226094_at; 235792_x_at; 241905_at; PIK3C2B 5287T-Cell 204484_at; PIK3C2G 5288 T-Cell 215129_at; PIK3C3 5289 T-Cell204297_at; 215394_at; 232086_at; 239300_at; PIK3CA 5290 T-Cell204369_at; 215212_at; PIK3CB 5291 T-Cell 212688_at; 217620_s_at; PIM15292 T-Cell 209193_at; PIK3CD 5293 T-Cell 203879_at; 211230_s_at; PIK3CG5294 T-Cell 206369_s_at; 206370_at; VAV 7409 T-Cell 206219_s_at; VAV27410 T-Cell 205536_at; 205537_s_at; 226063_at; VAV3 10451 T-Cell218806_s_at; 218807_at; 224221_s_at; ITK 3702 T-Cell 211339_s_at; SLP763937 T-Cell 205269_at; 205270_s_at; 244251_at; 244556_at; 244578_at; LAT27040 T-Cell 209881_s_at; 211005_at; PAG 55824 T-Cell 225622_at;225626_at; CBL 867 T-Cell 206607_at; 225231_at; 225234_at; 229010_at;243475_at; LCK 3932 T-Cell 204890_s_at; 204891_s_at; SHB 6461 T-Cell204656_at; 204657_s_at; 230459_s_at; 234794_at; 234795_at; 243595_at;PLCG1 5335 T-Cell LTBR 4055 LTBR 203005_at; 232819_s_at; 243400_x_at;NIK 9020 LTBR 205192_at; NIKBR 83696 LTBR 221672_s_at; 221836_s_at;56829_at; 229108_at; 237001_at; 237851_at; GADD45A 1647 Suvival203725_at; GADD45B 4616 Suvival 207574_s_at; 209304_x_at; 209305_s_at;213560_at; GADD45G 10912 Suvival 204121_at; XIAP 331 Suvival206536_s_at; 225858_s_at; 225859_at; 228363_at; 235222_x_at;243026_x_at; BCL-XL 598 Suvival 206665_s_at; 212312_at; 215037_s_at;231228_at; FLIP 8837 Suvival 208485_x_at; 209508_x_at; 209939_x_at;210563_x_at; 210564_x_at; 211316_x_at; 211317_s_at; 211862_x_at;214486_x_at; 214618_at; 217654_at; 237367_x_at; 239629_at; IAP 330Suvival 210538_s_at; 230499_at; SURVIVIN 332 Suvival 202094_at;202095_s_at; 210334_x_at; TNFRSF10C - DCR1 8794 Death 206222_at;211163_s_at; TRAF1 7185 Death 205599_at; 235116_at; RELA 5970 Death201783_s_at; 209878_s_at; 230202_at; TNFRSF1A - TNFR1 7132 Death207643_s_at; 241944_x_at; FADD 8772 Death 202535_at; CASP8 841 Death207686_s_at; 213373_s_at; 231218_at; CASP3 836 Death 202763_at;236729_at; BCL2 596 Death 203684_s_at; 203685_at; 207004_at;207005_s_at; 232210_at; 232614_at; 237837_at; 244035_at; CARMA1 84433Traf 2/6 223514_at; Complex BCL10 8915 Traf 2/6 205263_at; Complex MALT110892 Traf 2/6 208309_s_at; 210017_at; 210018_x_at; 238157_at; ComplexTRAF6 7186 Traf 2/6 204413_at; Complex TRAF2 7189 Traf 2/6 205558_at;Complex PAR1 2149 PAR 203989_x_at; PAR4 5074 PAR 204004_at; 204005_s_at;214090_at; 214237_x_at; 226223_at; 226231_at; 229515_at; CRK 1398SAPK/JNK 202224_at; 202226_s_at; CRKL 1399 SAPK/JNK 206184_at;212180_at; SHC 6464 SAPK/JNK 201469_s_at; 214853_s_at; SHC2 53358SAPK/JNK 206330_s_at; SHC3 25759 SAPK/JNK 213464_at; GRB2 2885 SAPK/JNK215075_s_at; 223049_at; 228572_at; SOS 6654 SAPK/JNK 212777_at;212780_at; 229261_at; 230337_at; 232883_at; 242018_at; 242682_at; HPK29448 SAPK/JNK 206571_s_at; 218181_s_at; 222547_at; 222548_s_at;238769_at; 244846_at; TAB1 10454 TAK1 203901_at; 233679_at; 235480_at;235827_at; Complex TAB2 23118 TAK1 210284_s_at; 212184_s_at; 233957_at;243557_at; Complex TAB3 257397 TAK1 227357_at; Complex TAK1 6885 TAK1206853_s_at; 206854_s_at; 211536_x_at; 211537_x_at; Complex NLK 51701NFkB 218318_s_at; 222589_at; 222590_s_at; IKK1 1147 NFkB 209666_s_at;IKK2 3551 NFkB 209341_s_at; 209342_s_at; 211027_s_at; IKK3 8517 NFkB209929_s_at; 36004_at; NFKB 4790 NFkB 209239_at; 239876_at; RELA 5970NFkB 201783_s_at; 209878_s_at; 230202_at; MKK4 6416 JNK 203265_s_at;203266_s_at; MKK7 5609 JNK 209951_s_at; 209952_s_at; 216206_x_at;226023_at; 226053_at; JNK 5599 JNK 210477_x_at; 210671_x_at; 226046_at;226048_at; 243280_at; MAPK9 5601 JNK 203218_at; 210570_x_at; 225781_at;MAPK10 5602 JNK 204813_at; DUSP8 1850 JNK 206374_at; IRS1 3667 JNK204686_at; 235392_at; SMC 9918 JNK 201774_s_at; HNRPK 3190 JNK200097_s_at; 200775_s_at; 200097_s_at; TP53 7157 JNK 201746_at;211300_s_at; 224185_at; ATF2 1386 JNK 205446_s_at; 212984_at; ELK1 2002JNK 203617_x_at; 210376_x_at; 210850_s_at; CJUN 3725 JNK 201464_x_at;201465_s_at; 201466_s_at; 213281_at; NFAT4 4775 JNK 207416_s_at;210555_s_at; 210556_at; 229223_at; NFATC1 4772 JNK 208196_x_at;209664_x_at; 210162_s_at; 211105_s_at; NLK 51701 WNT 218318_s_at;222589_at; 222590_s_at; CTBP1 1487 WNT 203392_s_at; 212863_x_at;213980_s_at; 243180_at; CBP 1387 WNT 202160_at; 211808_s_at; 235858_at;237239_at; TCF 3172 WNT 208429_x_at; 214832_at; 214851_at; 216889_s_at;230914_at; GROUCHO 7091 WNT 204872_at; 214688_at; 216997_x_at;233575_s_at; 235765_at; HIPK2 28996 WNT 213763_at; 219028_at; 224016_at;224065_at; 224066_s_at; 225097_at; 225115_at; 225116_at; 225368_at;240294_at; cMYB 4602 WNT 204798_at; 215152_at; ATF2 1386 ALK205446_s_at; 212984_at; CSX 1482 ALK 206578_at; GATA4 2626 ALK205517_at; 230855_at; 243692_at; MAP2K6 5608 p38 205698_s_at; p38MAPK5594 p38 208351_s_at; 212271_at; 224620_at; 224621_at; 229847_at;242106_at; MNK1 8569 p38 209467_s_at; 243256_at; PRAK 8550 p38212871_at; HSP27 6294 p38 201747_s_at; 201748_s_at; 213635_s_at; MAPKAP29261 p38 201460_at; 201461_s_at; 215050_x_at; PLA2 5320 p38 203649_s_at;STAT1 6772 p38 200887_s_at; 209969_s_at; AFFX-HUMISGF3A/M97935_3_at;AFFX- HUMISGF3A/M97935_5_at; AFFX-HUMISGF3A/M97935_MA_at; AFFX-HUMISGF3A/M97935_MB_at; 232375_at; AFFX-HUMISGF3A/M97935_3_at; AFFX-HUMISGF3A/M97935_5_at; AFFX-HUMISGF3A/M97935_MA_at; AFFX-HUMISGF3A/M97935_MB_at; MAX 4149 p38 208403_x_at; 209331_s_at;209332_s_at; 210734_x_at; 214108_at; 222174_at; MYC 4609 p38202431_s_at; 239931_at; 244089_at; ELK1 2002 p38 203617_x_at;210376_x_at; 210850_s_at; CHOP 2521 p38 200959_at; 215744_at;217370_x_at; 231108_at; MEF2 4205 p38 208328_s_at; 212535_at; 214684_at;239571_at; 242176_at; MEF3 4206 p38 MEF4 4207 p38 205124_at; 209926_at;MEF5 4208 p38 207968_s_at; 209199_s_at; 209200_at; 236395_at;239938_x_at; 239966_at; 244230_at; MEF6 4209 p38 203003_at; 203004_s_at;225641_at; ATF2 1386 p38 205446_s_at; 212984_at; MSK1 9252 p38204633_s_at; 204635_at; HMG14 3150 p38 200943_at; 200944_s_at; CREB 1385p38 204312_x_at; 204313_s_at; 204314_s_at; 214513_s_at; 243625_at;

TABLE 2 TAK inhibitor sensitivity determining signature including theinformative genes that differentiate 3 subclasses of DLBCL patients GeneGene Symbol Entrez Pathway U133A/B Group TNFR1 7132 TNF 207643_s_at; ATNFR2 7133 TNF 203508_at; A TRADD 8717 TNF 1729_at; 205641_s_at; AA TANK10010 TNF 207616_s_at; 209451_at; 210458_s_at; EEE RAIDD 8738 TNF209833_at; B PROCASP2 835 TNF 208050_s_at; 209811_at; 211140_s_at;34449_at; 226032_at; BBBBC UBC13 7334 TNF 201523_x_at; 201524_x_at;212751_at; EEE TLR2 7097 TLRs 204924_at; E TLR4 7099 TLRs 221060_s_at;224341_x_at; 232068_s_at; EEE TLR7 51284 TLRs 220146_at; 222952_s_at; EETLR10 81793 TLRs 223750_s_at; 223751_x_at; FF MYD88 4615 TLRs 209124_at;C TOLLIP 54472 TLRs 217930_s_at; 233881_s_at; ED IRAK 3654 TLRs201587_s_at; E PKR 5610 TLRs 204211_x_at; E TBK1 29110 TLRs 218520_at; ETGFB 7040 TGF-beta 203085_s_at; C IL1R 3554 IL1 202948_at; E TOLLIP54472 IL1 217930_s_at; 233881_s_at; ED MYD88 4615 IL1 209124_at; C CD19930 B-Cell 206398_s_at; F CD45 5788 B-Cell 207238_s_at; 212587_s_at;212588_at; AAA CD79A 973 B-Cell 205049_s_at; F CD79B 974 B-Cell205297_s_at; F LYN 4067 B-Cell 202625_at; 202626_s_at; 210754_s_at;239555_at; EEED SHP1 8431 B-Cell 206410_at; B SYK 6850 B-Cell207540_s_at; 209269_s_at; 226068_at; 244023_at; FFFF GAB1 2549 B-Cell207112_s_at; 242572_at; BE SHP2 5781 B-Cell 205868_s_at; 209895_at;209896_s_at; 212610_at; DDEE CSK 1445 B-Cell 202329_at; C PAG 55824B-Cell 225622_at; 225626_at; DD VAV 7409 B-Cell 206219_s_at; C VAV2 7410B-Cell 205536_at; 226063_at; FF GRB2 2885 B-Cell 215075_s_at; 223049_at;EE BLNK 29760 B-Cell 207655_s_at; 244172_at; FF SOS 6654 B-Cell212777_at; 212780_at; 229261_at; 230337_at; CCDDDE 232883_at; 242018_at;PLCG2 5336 B-Cell 204613_at; C PKCB 5579 B-Cell 207957_s_at;209685_s_at; 227817_at; 227824_at; 228795_at; DDDDD PRKCQ 5588 B-Cell210038_at; 210039_s_at; AB PRKCQ 5588 T-Cell 210038_at; 210039_s_at; ABPKCB 5579 T-Cell 207957_s_at; 209685_s_at; 227817_at; 227824_at;228795_at; DDDDD CD28 940 T-Cell 206545_at; 211856_x_at; 211861_x_at;AAA CD3 917 T-Cell 206804_at; A CD3E 916 T-Cell 205456_at; A CD3D 915T-Cell 213539_at; A CD4 920 T-Cell 203547_at; A UBC4 7322 T-Cell201343_at; 201345_s_at; 215604_x_at; 240139_at; FFDC UBC5 6923 T-Cell200085_s_at; 200085_s_at; EE CIAP1 329 T-Cell 202076_at; E CIAP2 330T-Cell 210538_s_at; 230499_at; EE CD8 925 T-Cell 205758_at; A CD8B 926T-Cell 207979_s_at; 215332_s_at; AE CD45 5788 T-Cell 207238_s_at;212587_s_at; 212588_at; AAA ZAP70 7535 T-Cell 214032_at; A FYN 2534T-Cell 210105_s_at; 212486_s_at; 216033_s_at; 217697_at; 243006_at;AAABA CLTA4 1493 T-Cell 221331_x_at; 231794_at; 234362_s_at; 236341_at;AAAA PI3k 5286 T-Cell 213070_at; 235792_x_at; 241905_at; EDD PIK3C2B5287 T-Cell 204484_at; D PIK3C2G 5288 T-Cell 215129_at; B PIK3C3 5289T-Cell 204297_at; 215394_at; 239300_at; EBA PIK3CA 5290 T-Cell204369_at; 215212_at; EE PIK3CB 5291 T-Cell 212688_at; 217620_s_at; DDPIM1 5292 T-Cell 209193_at; E PIK3CD 5293 T-Cell 203879_at; 211230_s_at;CC PIK3CG 5294 T-Cell 206369_s_at; 206370_at; DD VAV 7409 T-Cell206219_s_at; C VAV2 7410 T-Cell 205536_at; 226063_at; FF VAV3 10451T-Cell 218806_s_at; 218807_at; EE ITK 3702 T-Cell 211339_s_at; A SLP763937 T-Cell 205269_at; 205270_s_at; 244251_at; 244556_at; AAAA LAT 27040T-Cell 209881_s_at; 211005_at; AA PAG 55824 T-Cell 225622_at; 225626_at;DD CBL 867 T-Cell 206607_at; 225231_at; 225234_at; 229010_at; 243475_at;BCCCD LCK 3932 T-Cell 204890_s_at; 204891_s_at; AA SHB 6461 T-Cell204656_at; 204657_s_at; DB LTBR 4055 LTBR 203005_at; B NIK 9020 LTBR205192_at; D NIKBR 83696 LTBR 221672_s_at; 221836_s_at; 56829_at; CCCGADD45A 1647 Suvival 203725_at; E GADD45B 4616 Suvival 207574_s_at;209304_x_at; 209305_s_at; EEE XIAP 331 Suvival 206536_s_at; 225858_s_at;225859_at; 228363_at; BEEEEE 235222_x_at; 243026_x_at; BCL-XL 598Suvival 206665_s_at; 212312_at; 215037_s_at; EEE FLIP 8837 Suvival208485_x_at; 209508_x_at; 209939_x_at; AAAAAAAAA 210563_x_at;210564_x_at; 211316_x_at; BBAA 211317_s_at; 211862_x_at; 214486_x_at;214618_at; 217654_at; 237367_x_at; 239629_at; IAP 330 Suvival210538_s_at; 230499_at; EE SURVIVIN 332 Suvival 202094_at; 202095_s_at;210334_x_at; EEB TNFRSF10C - DCR1 8794 Death 206222_at; B TRAF1 7185Death 205599_at; 235116_at; DD RELA 5970 Death 201783_s_at; 209878_s_at;CC TNFRSF1A - TNFR1 7132 Death 207643_s_at; A FADD 8772 Death 202535_at;E CASP8 841 Death 207686_s_at; 213373_s_at; EA CASP3 836 Death202763_at; E BCL2 596 Death 203685_at; 207005_s_at; 232210_at;232614_at; 244035_at; EEEEE CARMA1 84433 Traf 2/6 223514_at; E ComplexBCL10 8915 Traf 2/6 205263_at; F Complex MALT1 10892 Traf 2/6208309_s_at; 210017_at; 210018_x_at; EEE Complex TRAF6 7186 Traf 2/6204413_at; E Complex TRAF2 7189 Traf 2/6 205558_at; D Complex PAR1 2149PAR 203989_x_at; B PAR4 5074 PAR 204004_at; 204005_s_at; 226223_at;226231_at; FFFF CRK 1398 SAPK/JNK 202224_at; 202226_s_at; EE CRKL 1399SAPK/JNK 206184_at; 212180_at; BC SHC 6464 SAPK/JNK 201469_s_at;214853_s_at; DA SHC3 25759 SAPK/JNK 213464_at; B GRB2 2885 SAPK/JNK215075_s_at; 223049_at; EE SOS 6654 SAPK/JNK 212777_at; 212780_at;229261_at; 230337_at; CCDDDE 232883_at; 242018_at; HPK2 9448 SAPK/JNK206571_s_at; 218181_s_at; 222547_at; DDDDDD 222548_s_at; 238769_at;244846_at; TAB1 10454 TAK1 203901_at; 233679_at; DE Complex TAB2 23118TAK1 210284_s_at; 212184_s_at; 243557_at; BAA Complex TAB3 257397 TAK1227357_at; E Complex TAK1 6885 TAK1 206853_s_at; 206854_s_at;211536_x_at; BBBB Complex 211537_x_at; NLK 51701 NFkB 218318_s_at;222589_at; 222590_s_at; DDD IKK1 1147 NFkB 209666_s_at; E IKK2 3551 NFkB209341_s_at; 209342_s_at; 211027_s_at; CDD IKK3 8517 NFkB 209929_s_at;36004_at; EC NFKB 4790 NFkB 209239_at; 239876_at; CD RELA 5970 NFkB201783_s_at; 209878_s_at; CC MKK4 6416 JNK 203265_s_at; 203266_s_at; BEMKK7 5609 JNK 216206_x_at; 226053_at; DD JNK 5599 JNK 226046_at;226048_at; EE MAPK9 5601 JNK 203218_at; 210570_x_at; 225781_at; EEDMAPK10 5602 JNK 204813_at; B DUSP8 1850 JNK 206374_at; C IRS1 3667 JNK204686_at; 235392_at; DD SMC 9918 JNK 201774_s_at; C HNRPK 3190 JNK200097_s_at; 200775_s_at; 200097_s_at; EEE TP53 7157 JNK 201746_at;211300_s_at; DD ATF2 1386 JNK 205446_s_at; 212984_at; DE ELK1 2002 JNK203617_x_at; 210376_x_at; 210850_s_at; CBB cJUN 3725 JNK 201464_x_at;201465_s_at; 201466_s_at; ABAB 213281_at; NFAT4 4775 JNK 207416_s_at;210555_s_at; 210556_at; DDD NFATC1 4772 JNK 208196_x_at; 210162_s_at;211105_s_at; ECC NLK 51701 WNT 218318_s_at; 222589_at; 222590_s_at; DDDCTBP1 1487 WNT 203392_s_at; 212863_x_at; 213980_s_at; CCC CBP 1387 WNT202160_at; 237239_at; CD TCF 3172 WNT 208429_x_at; 214832_at; 214851_at;BBBE 216889_s_at; GROUCHO 7091 WNT 204872_at; 214688_at; 216997_x_at;DDDDD 233575_s_at; 235765_at; 213763_at; 219028_at; 225097_at; HIPK228996 WNT 225116_at; 225368_at; BBBBB cMYB 4602 WNT 204798_at; E ATF21386 ALK 205446_s_at; 212984_at; DE MAP2K6 5608 p38 205698_s_at; Ep38MAPK 5594 p38 208351_s_at; 212271_at; 224621_at; BBD MNK1 8569 p38209467_s_at; 243256_at; CB PRAK 8550 p38 212871_at; E HSP27 6294 p38201747_s_at; 201748_s_at; 213635_s_at; CCB MAPKAP2 9261 p38 201460_at;201461_s_at; 215050_x_at; BBB STAT1 6772 p38 200887_s_at; 209969_s_at;AFFX- AAAAAAAAA HUMISGF3A/M97935_3_at; AA AFFX-HUMISGF3A/M97935_5_at;AFFX-HUMISGF3A/M97935_MA_at; AFFX-HUMISGF3A/M97935_MB_at; 232375_at;AFFX-HUMISGF3A/M97935_3_at; AFFX-HUMISGF3A/M97935_5_at;AFFX-HUMISGF3A/M97935_MA_at; AFFX-HUMISGF3A/M97935_MB_at; MAX 4149 p38208403_x_at; 209331_s_at; 209332_s_at; DDCDBB 210734_x_at; 214108_at;222174_at; MYC 4609 p38 202431_s_at; E ELK1 2002 p38 203617_x_at;210376_x_at; 210850_s_at; CBB CHOP 2521 p38 200959_at; 217370_x_at;231108_at; CCC MEF2 4205 p38 208328_s_at; 212535_at; 214684_at;239571_at; DDDDD 242176_at; MEF4 4207 p38 205124_at; F MEF5 4208 p38207968_s_at; 209199_s_at; 209200_at; DDDDDDD 236395_at; 239938_x_at;239966_at; 244230_at; ATF2 1386 p38 205446_s_at; 212984_at; DE MSK1 9252p38 204633_s_at; 204635_at; EE HMG14 3150 p38 200943_at; 200944_s_at; FFCREB 1385 p38 204312_x_at; 204313_s_at; 204314_s_at; EEEC 214513_s_at;

In still another aspect, the invention includes a method of selecting apatient having a tumour that is susceptible to treatment with a TAK1inhibitor. The method can include determining if the patient has agenetic mutation of a t(14;18)(q32;q21) translocation, at(11;18)(q21;q21) translocation, a t(1;14)(p22;q32) translocation, oramplification of chromosome 18, whereby the presence of a mutationindicates the tumour is susceptible to treatment.

Alternatively, the method can include determining if the patient has aderegulated TAK1 signalling transduction molecule, wherein the presenceof the deregulated TAK1 signalling transduction molecule is anindication that the patient is susceptible to treatment with a TAK1inhibitor.

In any of the methods described herein, the TAK1 inhibitor can beadministered either as a single agent or in combination with otheranti-cancer agents or anti-cancer antibodies.

In another aspect, the invention includes a kit for predicting apatient's response to a TAK1 inhibitor, said kit comprising (a) one ormore phospho-specific antibodies against a TAK1 signal transductionmolecule, and (b) a reagent suitable for detecting binding of saidantibodies to the TAK1 signal transduction molecule.

In yet another aspect, the invention includes methods to classify atumor as a TAK1 inhibitor sensitive tumor. By measuring the relativelevels of particular deregulated TAK1 signalling transduction genes orproteins in tumour tissue it is possible to determine if the tumor isresponsive to a TAK1 inhibitor. The present invention can be used topredict the suitability of administering a TAK1 inhibitor to a cancerpatient.

According to one aspect of the present invention there is provided amethod of selecting a mammal having or suspected of having a tumour fortreatment with a TAK1 inhibitor drug. The method includes providing abiological sample from a subject having a B cell tumour, a solid tumor,or a T cell leukemia and testing the biological sample for expression ofany one of the genes listed in Table 1 or Table 2, or their geneproducts, thereby to predict an increased likelihood of response to theTAK1 inhibitor drug. In one embodiment, the method includes testing thebiological sample for at least 5, 10, 20, 30, 40, 50 or 100 of the geneslisted in Table 1 or Table 2.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic of the TAK1 signaling pathway in B celllymphocytes (BCR) and T cell lymphocytes (TCR).

FIG. 2 shows a bar chart showing the effect of TAK1 knock down by shRNAon the viability of B-cell lymphoma cells with a t(14;18)(q32;q21)translocation.

FIG. 3 shows a bar chart showing the effect of a TAK1 kinase inhibitoron the viability of B-cell lymphoma cells with a t(14;18)(q32;21)translocation.

DETAILED DESCRIPTION

The present invention is based, in part, on the finding that certainlymphomas, in particular B cell tumors, solid tumors or T cellleukemia's, are selectively responsive to a TAK1 inhibitor.

Moreover, the invention includes identifying tumours carrying particularmutations including a t(14;18)(q32;q21) translocation, at(11;18)(q21;q21) translocation, a t(1;14)(p22;q32) translocation, anamplification of chromosome 18, an addition of chromosome 18q21, anamplification of specific regions (detected by comparative genomichybridization), changes in the subcellular localization, over- orunder-expression of a deregulated TAK1 signalling transduction molecule,or posttranscriptional modifications in the proteins containing TAK1pathway signaling molecules including MALT1, BCL-10, TAK1, TRAF6, CARD11, IRAK1, TAB 1, TAB2, TRAF2, IRAK4, API1, API2, API3, API4 (survivin),BCL2 or NF-kB target genes or deletion of specific regions containingAPI2. NF-kB target genes include any gene that is regulated by the NF-kBtranscription factor, for example a set of NF-KB target genes isprovided in the reference Dave S S et. al. N. Engl. J. Med. 2006;354(23): 2431-42. These tumours have been identified to be particularlysusceptible to treatment using a TAK1 inhibitor.

The identification of the above particular mutations of the presentinvention can be used to determine if a patient is a responder ornon-responder to a TAK1 inhibitor. By responders and non responders itis meant objective tumour responses according to the Union InternationalContre le Cancer/World Health Organization (U ICC/WHO) criteria arecategorised as follows: complete response (CR): no residual tumour inall evaluable lesions; partial response (PR): residual tumour withevidence of chemotherapy-induced 50% or greater decrease under baselinein the sum of all measurable lesions and no new lesions; stable disease(SD): residual tumour not qualified for CR; and progressive disease(PD): residual tumour with evidence of 25% or greater increase underbaseline in the sum of all measurable lesions or appearance of newlesions. As defined herein non-responders are PD.

Deregulated TAK1 Signal Transduction Molecules

The invention further includes identifying a tumour for a deregulatedTAK1 signaling transduction molecule. A deregulated TAK1 signalingtransduction molecule is any molecule that is directly or indirectlymodified, for example activated or deactivated, in the MALT pathwaycompared to a normal cell. See FIG. 1. A deregulated TAK1 signalingmolecule also includes tumor cells that have a deregulated TAK1signaling molecule, for example, molecules that are over orunder-expressed in signalling pathways involving TAK1. Such signallingpathways include antigen receptor signalling on T and B cells, IL-1 andTLR family signalling, TNF signalling, etc.

Tumours having deregulated TAK1 signaling molecules have been identifiedto be particularly susceptible to treatment using a TAK1 inhibitor. Thepresent invention includes a number of different biomarkers that can beused to predict a patient's responsiveness to a TAK1 inhibitor. Thebiomarkers of the invention include genetic mutations whereby thepresence of a mutation indicates that the tumour is susceptible totreatment. Examples of genetic mutations that lead to deregulated TAK1signaling are the t(14;18)(q32;q21) translocation that causes MALT1 (andBCL2) to be overexpressed, the t(11;18)(q21;q21) translocation thatresults in a fusion protein of MALT1 with API2 and the t(1;14)(p22;q32)translocation that results in overexpression of BCL-10. Further examplesof genetic mutations that lead to deregulated TAK1 signaling includeamplification of chromosome 18 resulting in overexpression of MALT1 orBCL2, and amplifications or deletions of specific regions identified bycomparative genomic hybridization containing key components of the TAK1signalling pathway including MALT1, BCL-10, TAK1, TRAF6, TRAF2, TAB1,TAB2, CARD11, IRAK1, IRAK4, API1, API2, API3, API4 and NF-kB targetgenes.

The biomarkers of the invention also include deregulated TAK1 signallingtransduction molecules, wherein the presence of the deregulated TAK1signalling transduction molecule is an indication that the patient issusceptible to treatment with a TAK1 inhibitor. Examples of deregulatedTAK1 signal transduction molecules include molecules modified byposttranslational alterations such as phosphorylation includingphosphorylated TAK1, phosphorylated IKKbeta, phosphorylated p65,phosphorylated MKK4, phosphorylated MKK6, phosphorylated p38 andphosphorylated JNK. Other molecules that serve as deregulated TAK1signal transduction molecules include molecules modified byubiquitinylation including ubiquitinylated TRAF6, ubiquitinylatedIKKgamma and ubiquitinylated IkappaBalpha. Other markers that serve asderegulated TAK1 signal transduction molecules include alterations insubcellular localization such as translocation of molecules such asBCL-10, API4, p65 and RelA from the cytoplasm to the nucleus.

A deregulated TAK1 signaling molecule also includes any molecule that isover- or under-expressed in the TAK1 signalling pathway. By measuringthe relative levels of one or more deregulated TAK1 signaling moleculesas shown in Table 1 or Table 2, i.e., measuring gene expression orprotein expression or activity in a tumour tissue it is possible todetermine if the tumor is responsive to a TAK1 inhibitor. The presentinvention can thus be used to predict the suitability of administering aTAK1 inhibitor to a cancer patient.

Assays

The present invention provides a number of biomarkers that can be usedto predict a patient's responsiveness to a TAK1 inhibitor. One exemplarymethod for detecting the presence of a biomarker includes obtaining atumour sample from a test subject and determining for the presence ofthe biomarker.

Any appropriate sample can be used to determine for the presence of abiomarker of the invention. In one example the sample is a suspected Bcell tumour and determination of whether that tumour has a geneticmutation is performed. Examples of genetic mutations include at(14;18)(q32;q21) translocation, a t(11;18)(q21;q21) translocation, at(1;14)(p22;q32), an amplification of chromosome 18, or addition ofchromosome 18q21. These markers can be characterized by fluorescent insitu hybridization, comparative genomic hybridization (CGH) and cDNAmicroarrays for gene expression profiling and copy number changes.

Detection of a Deregulated TAK1 Signal Transduction Pathway Molecule

Means of determining if a sample has a genetic mutation are known in theart. These methods include those described or claimed in the followingpublications, the entire disclosures of which are incorporated byreference herein. Methods to determine if the tumor has an amplificationof chromosome 18 are described in Haematologica. 2006; 91(2): 184-91. At(14;18) translocation can be determined interphase fluorescence in situhybridization (FISH) as described by Godon A et. al, Leukemia. 2003;17(1):255-9 or by Farter J L et. al, 1: Diagn Mol Pathol. 2001;10(4):214-22. A t(14;18)(q32;q21) translocation can be determined asdescribed in Davies et al., Chromosome Res. 2005; 13(3):237-48. Theexpression of AP12-MALT1 mRNA can be studied using reverse transcriptase(RT)-polymerase chain reaction (PCR) and nested PCR as described inSanchez-Izquierdo D et. al Blood 2003 101: 11 4539-4546 and Ye H et. alJournal of pathology 2005; 205: 293-301. A t(11;18)(q21;q21)translocation can be detected by RT-PCR of the AP12-MALT1 fusiontranscripts and a t(14;18)(q21;q21) translocation can be detected byinterphase fluorescence in situ hybridisation (FISH; Vysis Abott Labs).

The procedures and reagents needed to determine for a deregulated TAK1signal transduction molecule are known in the art. In one example, anagent of interest that can be used to detect a deregulated TAK1 signaltransduction molecule includes any molecule such as a peptidomimetic,protein, peptide, nucleic acid, small molecule, an antibody or otherdrug candidate, that can bind the protein. In one example, antibodiesthat are commercially available can be used to detect a deregulated TAK1signal transduction molecule. For example, phosphorylated (phos) TAK1,Phos IkB, Phos IKK, Phos P38 can be measured by using Phospho specificantibodies from Cell Signaling USA. Alternatively, a deregulated TAK1signal transduction molecule such as MALT and BCL-10 can be performedusing immunostaining with mouse monoclonal Antibodies.

Typically, the method includes determining from a tumour sample of atest patient for the presence of a deregulated TAK1 signal transductionpathway molecule. For example, phosphorylated-TAK1 can be visualized byreacting the proteins with antibodies such as monoclonal antibodiesdirected against the phosphorylated serine, threonine or tyrosine aminoacids that are present in the proteins. For example, monoclonalantibodies useful for isolating and identifyingphosphotyrosine-containing proteins are described in U.S. Pat. No.4,543,439.

Typically, antibodies used for visualizing a deregulated TAK1 signaltransduction molecule can be labeled by any procedure known in the art,for example, using a reporter molecule. A reporter molecule, as usedherein, is a molecule which provides an analytically identifiable signalallowing one of skill in the art to identify when an antibody has boundto a protein that it is directed against. Detection may be eitherqualitative or quantitative. Commonly used reporter molecules includefluorophores, enzymes, biotin, chemiluminescent molecules,bioluminescent molecules, digoxigenin, avidin, streptavidin orradioisotopes. Commonly used enzymes include horseradish peroxidase,alkaline phosphatase, glucose oxidase and beta-galactosidase, amongothers. The substrates to be used with these enzymes are generallychosen for the production, upon hydrolysis by the corresponding enzyme,of a detectable color change. For example, p-nitrophenyl phosphate issuitable for use with alkaline phosphatase reporter molecules; forhorseradish peroxidase, 1,2-phenylenediamine, 5-aminosalicylic acid ortoluidine are commonly used. Incorporation of a reporter molecule ontoan antibody can be by any method known to the skilled artisan.

After separation and visualizing the proteins, the amount of eachprotein species may be assessed by readily available procedures. Forexample, by using Western blot analysis which includeselectrophoretically separating proteins on a polyacrylamide gel, andafter detecting the separated proteins, the relative amount of eachprotein can be quantified by assessing its optical density.Alternatively, other methods such as FACS, immunohistochemistry,immunocytochemistry, fluorescence microscopy, ELISA, etc., can be usedeither for altered expression of naïve, posttranslationally modifiedproteins or for monitoring the alterations in the subcellularlocalization of the proteins.

In the methods of the invention one or more deregulated TAK1 signaltransduction pathway molecules can be detected. For example, an assaysystem can be set up which can detect for the presence of multiplederegulated TAK1 signal transduction pathway molecules.

Expression Profile

The invention also includes a method for determining an expressionprofile of an appropriate tumour sample to determine if that tumour islikely to be responsive to TAK1 inhibitor treatment. In one example, thepresent invention includes determining for the level of expression ofthe genes in Table 1 or Table 2 in the test tumour sample. The geneprofile obtained is compared against controls, i.e., expressionpatterns, which is indicative that a tumour is responsive to TAK1treatment. The gene sequences of each of the biomarkers listed in Table1 or Table 2 can be detected using agents that can be used tospecifically detect the gene or other biological molecules relating toit, for example, RNA transcribed from the gene or polypeptides encodedby the gene. Exemplary detection agents are nucleic acid probes, whichhybridize to nucleic acids corresponding to the gene, and antibodies.

The biomarkers listed in Table 1 or Table 2 are intended to also includenaturally occurring sequences including allelic variants and otherfamily members. The biomarkers of the invention also include sequencesthat are complementary to those listed sequences resulting from thedegeneracy of the code and also sequences that are sufficientlyhomologous and sequences which hybridize under stringent conditions tothe genes listed in Table 1 or Table 2. Conditions for hybridization areknown to those skilled in the art and can be found in Current Protocolsin Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Apreferred, non-limiting example of highly stringent hybridizationconditions are hybridization in 6× sodium chloride/sodium citrate (SSC)at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at50-65° C.

By “sufficiently homologous” it is meant a amino acid or nucleotidesequence of a biomarker which contains a sufficient or minimum number ofidentical or equivalent (e.g., an amino acid residue which has a similarside chain) amino acid residues or nucleotides to a second amino acid ornucleotide sequence such that the first and second amino acid ornucleotide sequences share common structural domains or motifs and/or acommon functional activity. For example, amino acid or nucleotidesequences which share common structural domains have at least about 50%homology, preferably 60% homology, more preferably 70%-80%, and evenmore preferably 90-95% homology across the amino acid sequences of thedomains and contain at least one and preferably two structural domainsor motifs, are defined herein as sufficiently homologous. Furthermore,amino acid or nucleotide sequences which share at least 50%, preferably60%, more preferably 70-80% or 90-95% homology and share a commonfunctional activity are defined herein as sufficiently homologous.

The comparison of sequences and determination of percent homologybetween two sequences can be accomplished using a mathematicalalgorithm. A preferred, non-limiting example of a mathematical algorithmutilized for the comparison of sequences is the algorithm of Karlin andAltschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-68, modified as inKarlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. Suchan algorithm is incorporated into the NBLAST and XBLAST programs(version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLASTnucleotide searches can be performed with the NBLAST program, score=100,wordlength=12 to obtain nucleotide sequences homologous to TRL nucleicacid molecules of the invention. BLAST protein searches can be performedwith the XBLAST program, score=50, wordlength=3 to obtain amino acidsequences homologous to the protein sequences encoded by the geneslisted in Table 1 or Table 2. To obtain gapped alignments for comparisonpurposes, Gapped BLAST can be utilized as described in Altschul et al.,(1997) Nucleic Acids Research 25(17):3389-3402. When utilizing BLAST andGapped BLAST programs, the default parameters of the respective programs(e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.Another preferred, non-limiting example of a mathematical algorithmutilized for the comparison of sequences is the ALIGN algorithm of Myersand Miller, CABIOS (1989). When utilizing the ALIGN program forcomparing amino acid sequences, a PAM120 weight residue table, a gaplength penalty of 12, and a gap penalty of 4 can be used.

Methods for Determining Nucleic Acid Sequences that are DifferentiallyExpressed in a Subject with Cancer

The invention provides a list of genes or gene products that can be usedto produce an expression profile signature which characteristicallypredicts TAK1 inhibitor sensitivity of a tumour cell. Any method knownin the art can be used to determine whether a tumour cell is responsiveto treatment with an TAK1 inhibitor.

In one embodiment, the method comprises determining mRNA and/or proteinlevel of the biomarkers of a mammal, such as by Northern blot analysis,reverse transcription-polymerase chain reaction (RT-PCR), in situhybridization, immunoprecipitation, Western blot hybridization, orimmunohistochemistry. According to the method, cells may be obtainedfrom a subject and the levels of the biomarker's protein or mRNA levelare determined and compared to a control.

In one embodiment, the method comprises using a nucleic acid probe todetermine whether a mammal is responsive to TAK1 inhibition. The methodincludes:

-   -   providing a nucleic acid probe comprising a nucleotide sequence,        for example, at least 10, 15, 25 or 40 nucleotides, and up to        all or nearly all of the coding sequence which is complementary        to a portion of the coding sequence of a nucleic acid sequence        listed in Table 1 or Table 2;    -   obtaining a tissue sample from a mammal having a cancerous        cells;    -   contacting the nucleic acid probe under stringent conditions        with RNA obtained from the sample (e.g., in a Northern blot or        in situ hybridization assay); and    -   comparing the amount of hybridization of the probe with RNA        derived from; wherein the amount of hybridization is indicative        of the presence of cancerous cells in the first tissue sample.

In another example, the methods of the invention include determiningexpression profiles with microarrays involves the following steps: (a)obtaining a mRNA sample from a subject and preparing labeled nucleicacids therefrom (the “target nucleic acids” or “targets”); (b)contacting the target nucleic acids with an array under conditionssufficient for the target nucleic acids to bind to the correspondingprobes on the array, for example, by hybridization or specific binding;(c) optional removal of unbound targets from the array; (d) detectingthe bound targets, and (e) analyzing the results, for example, usingcomputer based analysis methods, to indicate whether the mammal isresponsive to TAK1 inhibition treatment

In the method detailed above, the method includes obtaining mRNA fromthe mammal's tumour sample. RNA may be extracted from tissue or cellsamples by a variety of methods, for example, guanidium thiocyanatelysis followed by CsCl centrifugation (Chirgwin, et al., Biochemistry18:5294-5299, 1979). RNA from single cells may be obtained as describedin methods for preparing cDNA libraries from single cells (see, e.g.,Dulac, Curr. Top. Dev. Biol. 36:245, 1998; Jena, et al., J. Immunol.Methods 190:199, 1996).

The RNA sample can be further enriched for a particular species. In oneembodiment, for example, poly(A)+ RNA may be isolated from an RNAsample. In particular, poly-T oligonucleotides may be immobilized on asolid support to serve as affinity ligands for mRNA. Kits for thispurpose are commercially available, for example, the MessageMaker kit(Life Technologies, Grand Island, N.Y.).

In one embodiment, the RNA population may be enriched for sequences ofinterest, as detailed on Table 1 or Table 2. Enrichment may beaccomplished, for example, by primer-specific cDNA synthesis, ormultiple rounds of linear amplification based on cDNA synthesis andtemplate-directed in vitro transcription (see, e.g., Wang, et al., Proc.Natl. Acad. Sci. USA 86:9717, 1989; Dulac, et al., supra; Jena, et al.,supra).

The target molecules may be labeled to permit detection of hybridizationof the target molecules to a microarray. That is, the probe may comprisea member of a signal producing system and thus, is detectable, eitherdirectly or through combined action with one or more additional membersof a signal producing system. Examples of directly detectable labelsinclude isotopic and fluorescent moieties incorporated, usually by acovalent bond, into a moiety of the probe, such as a nucleotidemonomeric unit (e.g., dNMP of the primer), or a photoactive orchemically active derivative of a detectable label which can be bound toa functional moiety of the probe molecule.

In other embodiments, the target nucleic acid may not be labeled. Inthis case, hybridization may be determined, for example, by plasmonresonance (see, e.g., Thiel, et al., Anal. Chem. 69:4948, 1997).

Microarrays for use according to the invention include one or moreprobes of genes listed in Table 1 or Table 2.

The method described above results in the production of hybridizationpatterns of labeled target nucleic acids on the array surface. Theresultant hybridization patterns of labeled nucleic acids may bevisualized or detected in a variety of ways, with the particular mannerof detection selected based on the particular label of the targetnucleic acid. Representative detection means include scintillationcounting, autoradiography, fluorescence measurement, calorimetricmeasurement, light emission measurement, light scattering, and the like.

One such method of detection utilizes an array scanner that iscommercially available (Affymetrix, Santa Clara, Calif.), for example,the 417™ Arrayer, the 418™ Array Scanner, or the Agilent GeneArray™Scanner. This scanner is controlled from a system computer with aninterface and easy-to-use software tools. The output may be directlyimported into or directly read by a variety of software applications.Scanning devices are described in, for example, U.S. Pat. Nos. 5,143,854and 5,424,186.

Proteins

Detecting for the presence of a protein product encoded by one or moreof the biomarker genes listed in Table 1 or Table 2 can be done by usingany appropriate method known in the art. For example, an agent ofinterest that can be used to detect a particular protein of interest,for example using an antibody. The method for producing polyclonaland/or monoclonal antibodies that specifically bind to polypeptidesuseful in the present invention is known to those of skill in the artand may be found in, for example, Dymecki, et al., (J. Biol. Chem.267:4815, 1992); Boersma & Van Leeuwen, (J. Neurosci. Methods 51:317,1994); Green, et al., (Cell 28:477, 1982); and Arnheiter, et al.,(Nature 294:278, 1981).

In one embodiment, an immunoassay can be used to quantitate the levelsof proteins in cell samples. The invention is not limited to aparticular assay procedure, and therefore, is intended to include bothhomogeneous and heterogeneous procedures. Exemplary immunoassays thatmay be conducted according to the invention include fluorescencepolarization immunoassay (FPIA), fluorescence immunoassay (FIA), enzymeimmunoassay (EIA), nephelometric inhibition immunoassay (NIA),enzyme-linked immunosorbent assay (ELISA), and radioimmunoassay (RIA).

In another example, the presence of the marker protein in a tissuesample can be determined using immunohistochemical staining. For suchstaining, a multiblock of tissue may be taken from the biopsy or othertissue sample and subjected to proteolytic hydrolysis, employing suchagents as protease K or pepsin. In certain embodiments, it may bedesirable to isolate a nuclear fraction from the sample cells and detectthe level of the marker polypeptide in the nuclear fraction.

In yet another embodiment, the invention contemplates using a panel ofantibodies that are generated against the marker polypeptides of thisinvention. Such a panel of antibodies may be used as a reliablediagnostic probe for determining if a tumour is responsive to treatmentwith an TAK1 inhibitor.

Data Analysis

To facilitate the sample analysis operation, the data obtained by thereader from the device may be analyzed using a digital computer.Typically, the computer will be appropriately programmed for receipt andstorage of the data from the device, as well as for analysis andreporting of the data gathered, for example, subtraction of thebackground, deconvolution of multi-color images, flagging or removingartifacts, verifying that controls have performed properly, normalizingthe signals, interpreting fluorescence data to determine the amount ofhybridized target, normalization of background and single base mismatchhybridizations, and the like.

In one embodiment, a system comprises a search function that allows oneto search for specific patterns, for example, patterns relating todifferential gene expression, for example, between the expressionprofile of the test tumour cell and the expression profile of a tumourcell that is responsive to treatment with an TAK1 inhibitor. A systemmay also allow one to search for patterns of gene expression betweenmore than two samples. Comparison of the expression levels of one ormore genes characteristic of responsiveness to an TAK1 inhibitor withreference expression levels, for example, expression levels that arecharacteristic of susceptibility to an TAK1 inhibitor may be conductedusing computer systems.

Subtyping Diffuse Large B-Cell Lymphoma (DLBL/DLBCL) Patients toDetermine if the Patient is Sensitive to a TAK1 Inhibitor

The present invention can be used to subtype DLBCL patients in order todetermine if the patients are sensitive or likely insensitive to a TAK1inhibitor. Specifically, patients can be categorized to determine if thepatients fall within 3 distinct subclasses based on their expressionpattern of TAK1 genes. A patient sample that falls within Groups 1 and 3as described below are believed to be TAK1 sensitive, while a patientsample that falls within Group 2 is likely to be TAK1 insensitive. Amethod for subtyping DLBCL patients is described below. Thus, theinvention includes providing a test DLBCL sample and determining whetherthe sample falls within Groups 1, 2 or 3.

-   -   The method includes:    -   mapping genes of Table 1 to Affymetrix probesets based on the        annotations available from Affymetrix        (http://www.affymetrix.com/analysis/index.affx);    -   providing an Affymetrix U133A/B gene chip having gene expression        data of 176 newly diagnosed diffuse large B cell lymphoma        (DLBCL) patients;    -   verifying data quality such that 113 samples (Table 3) are kept        for further analysis; and    -   performing sample clustering such that three groups generated,        wherein samples that fall within Groups 1 and 3 are TAK1        sensitive, while a sample falling within Group 2 is TAK1        insensitive.    -   To test whether a DLBCL patient sample falls within Group 1, 2        or 3 the method includes:    -   providing a test DBLCL patient sample;    -   providing a data verified U133A/B gene chip;    -   normalizing the test sample with the 113 samples of Table 3;    -   clustering the test sample and the 113 samples including the        sensitivity determining signature gene set as in Table 2,        wherein if the test sample falls within Groups 1 and 3 the        sample is TAK1 sensitive, whereas if the test sample falls        within Group 2 the sample is TAK1 insensitive.

Details of how to Perform the Above Method are Provided Below: 1. TAK1Pathways Genes

Genes in TAK1 pathways can be assembled based on the public information.The genes that are involved in the signaling of ALK, FAS, MAP kinase,IL-1 receptor, TGF-beta, TNF receptor, thrombin and protease-activatedreceptor, Toll-like receptor, WNT, and antigen receptor are included.These genes can be mapped to Affymetrix probesets based on theannotations available from Affymetrix(http://www.affymetrix.com/analysis/index.affx) (Table 1)

2. Gene Expression Data

The gene expression data of 176 newly diagnosed diffuse large B celllymphoma (DLBCL) patients generated with Affymetrix U133A/B gene chipare publicly available by Margaret Shipp's group at Dana Faber CancerInstitute (Molecular profiling of diffuse large B-cell lymphomaidentifies robust subtypes including one characterized by hostinflammatory response Blood 105(5) 1851-1861). The raw data can bedownloaded from http://www.broad.mit.edu/cgi-bin/cancer/datasets.cgi,and further processed and analyzed as described below.

3. Data Preprocessing and Analysis 3.1 QC:

In order to verify data quality, and generate gene expression results,the raw data (.CEL files) of the DLBCL samples can be loaded intoAffymetrix Expression Console 1.0 (Affymetrix Inc.) and analyzed usingMAS5 algorithm. The following criteria are used to filter out sampleswith low quality data: 1) scaling factor <4; 2) rawQ <5; 3) 3′/5′ ratiofor both actin and GAPDH <5; 4) percentage of present call >20 for chipA or >10 for chip B. As a result of the QC procedure, 113 samples (Table3) are kept for further analysis.

3.2 Normalization:

Array normalization: The parameters for MAS5 algorithm are set tonormalize each array using all probesets on the array, and the trimmedmean value for each array is preset to 100.

Probeset normalization: The expression matrix generated by MAS5 can thenbe further normalized so that the mean of each probeset is centered tozero.

3.3 Sample Clustering:

For unsupervised clustering analysis, the normalized expression matrixis loaded into GeneSpring GX 7.3.1 (Agilent Inc.). A 2-way hierarchicalclustering is performed using only probeset identifications from table2. Spearman correlation was used as the similarity measure in theclustering. The result from clustering reveals three subtypes, Group 1,2 and 3.

4. Test DLBCL Samples

New test patient samples can be profiled using affymetrix U133A/B chips.After the data has been inspected following the same quality control(QC) procedure as described above 3.1, they can be added into theaffymetrix U133A/B chip data with 113 samples (Table 3). The new testsample set (113 plus test sample) will be analyzed following the sameprocess as outlined above 3.2-3.3. The new test samples will beclustered into one of the Groups 1-3. If the test sample falls withinGroup 1 and 3, the patient is likely to be TAK1 sensitive. If the testsample falls within Group 2, the patient is likely to be TAK1insensitive.

TABLE 3 DLBCL.NEW.206 DLBCL.NEW.210 DLBCL.NEW.211 DLBCL.NEW.215DLBCL.NEW.219 DLBCL.NEW.230 DLBCL.NEW.232 DLBCL.NEW.239 DLBCL.NEW.240DLBCL.NEW.242 DLBCL.NEW.244 DLBCL.NEW.246 DLBCL.NEW.250 DLBCL.NEW.251DLBCL.NEW.254 DLBCL.NEW.259 DLBCL.NEW.261 DLBCL.NEW.262 DLBCL.NEW.267DLBCL.NEW.268 DLBCL.NEW.269 DLBCL.NEW.270 DLBCL.NEW.271 DLBCL.NEW.272DLBCL.NEW.277 DLBCL.NEW.279 DLBCL.NEW.280 DLBCL.NEW.282 DLBCL.NEW.283DLBCL.NEW.284 DLBCL.NEW.285 DLBCL.NEW.286 DLBCL.NEW.290 DLBCL.NEW.291DLBCL.NEW.295 DLBCL.NEW.300 DLBCL.NEW.301 DLBCL.NEW.303 DLBCL.NEW.304DLBCL.NEW.307 DLBCL.NEW.309 DLBCL.NEW.311 DLBCL.NEW.312 DLBCL.NEW.313DLBCL.NEW.332 DLBCL.NEW.333 DLBCL.NEW.336 DLBCL.NEW.338 DLBCL.NEW.339DLBCL.NEW.340 DLBCL.NEW.344 DLBCL.NEW.345 DLBCL.NEW.347 DLBCL.NEW.348DLBCL.NEW.349 DLBCL.NEW.350 DLBCL.NEW.353 DLBCL.NEW.357 DLBCL.NEW.359DLBCL.NEW.361 DLBCL.NEW.404 DLBCL.NEW.405 DLBCL.NEW.408 DLBCL.NEW.411DLBCL.NEW.412 DLBCL.NEW.416 DLBCL.NEW.417 DLBCL.NEW.418 DLBCL.NEW.421DLBCL.NEW.422 DLBCL.NEW.423 DLBCL.NEW.426 DLBCL.NEW.427 DLBCL.NEW.430DLBCL.NEW.432 DLBCL.NEW.433 DLBCL.NEW.435 DLBCL.NEW.436 DLBCL.NEW.441DLBCL.NEW.443 DLBCL.NEW.445 DLBCL.NEW.448 DLBCL.NEW.449 DLBCL.NEW.451DLBCL.NEW.452 DLBCL.NEW.454 DLBCL.NEW.455 DLBCL.NEW.458 DLBCL.NEW.460DLBCL.NEW.461 DLBCL.NEW.462 DLBCL.NEW.463 DLBCL.NEW.467 DLBCL.NEW.470DLBCL.NEW.474 DLBCL.NEW.475 DLBCL.NEW.476 DLBCL.NEW.477 DLBCL.NEW.479DLBCL.NEW.481 DLBCL.NEW.482 DLBCL.NEW.485 DLBCL.NEW.496 DLBCL.NEW.497DLBCL.NEW.498 DLBCL.NEW.502 DLBCL.NEW.503 DLBCL.NEW.504 DLBCL.NEW.507DLBCL.NEW.509 DLBCL.NEW.514 DLBCL.NEW.609 DLBCL.NEW.617

TAK1 Inhibitors

TAK1 inhibitors are known in the art, for example, the TAK1 inhibitorcan include, for example, a peptide, an antibody, an antisense moleculeor a small molecule. TAK1 inhibitors useful in the present inventioninclude but are not limited to, those described or claimed in thefollowing publications the entire disclosures of which are incorporatedby reference herein. Examples of small molecule TAK1 inhibitors includezearalenones those disclosed in WO 2002048135, TAK1 short interferingRNA (siRNA) are described in Takaesu et. al J Mol. Biol. 2003;326(1):105-15 and an inactive mutant of TAK1 is described in Thiefes et.al., J Biol. Chem. 2005; 280(30):27728-41.

The TAK1 inhibitor can be administered either as a single agent or incombination with other anti-cancer agents or anti-cancer antibodiesincluding CHOP or rituximab.

EXAMPLES Example 1 The Following Example was Performed to DetermineInhibition of Cell growth by a TAK1 inhibitor comprising of shRNAAgainst TAK1.

TAK1 shRNAs and scrambled shRNAs were designed using the Ref Seq #:NM_(—)003188 and constructed in to pSIREN RetroQ retroviral vector(Clontech). Initial validation of the shRNAs was done in a HeLa cellline by co-transfection of TAK1 shRNA with NF-KB Luc vector (Clontech'sMercury profiling systems). Takaesu et. al J Mol. Biol. 2003;326(1):105-15. have demonstrated that TAK1 is critical for the NF-kBactivation in HeLa cells. The shRNA construct that showed about 70%inhibition of NF-KB Luc assay and inhibited TAK1 protein levels by 70%was selected for further evaluation of the role of TAK in maintainingthe survival of lymphoma cells. This construct along with the scrambledconstruct was transfected along with gag/pol plasmid and pVSV-G in tothe 293T cells. The viral supernatant was harvested and used to infectthe lymphoma cells in culture dishes. The four cell lines (OCI-LY19,DOHH2, Karpas231 and WSU-NHL carry the t(14;18) translocation) wereplated at 25,000 cells/well in flat-bottomed 24 well plates and treatedwith 1 ml of viral supernatant from TAK1 shRNA and scrambled shRNA intriplicate and incubated for a total of 72 hours. Following theincubation period, the extent of cell survival was measured by adding1/10 (vol/vol) AlamarBlue reagent to every well and incubating theplates for a further 4 hours. The reaction was stopped by the additionof SDS to a final concentration of 0.1%. Fluorescence was measured at545 nm (excitation) and 600 nm (emission). The cell survival data isrepresented in FIG. 2 as percent of live cells as compared to thescrambled shRNA treated groups.

Example 2 The following example was performed to determine inhibition ofcell growth by a TAK1 inhibitor comprising a small molecule.

In order to demonstrate that the kinase function of TAK1 is critical forthe Lymphoma cell survival, a small molecule inhibitor of TAK1 wastested in the same set of Lymphoma cell lines as above carrying thet(14;18) chromosomal translocation. The chemical name of the compound is3-[(aminocarbonyl)amino]-5-(4-{[4-(2-methoxyethyl)piperazin-1-yl]methyl}phenyl)thiophene-2-carboxamide.

More specifically, cell lines (OCI-LY19, DOHH2, Karpas231, WSU-NHL andSUDHL4 carry the t(14;18) translocation) were plated at 10,000cells/well in flat-bottomed 96 well plates and dosed with test compoundsin triplicate over a 10 point dosing range from 0 to 30 μmolesL⁻¹. Allcell lines were incubated with test compounds for a total of 72 hours.Background levels were determined for a control (undosed) plate within 2hours of dosing test compounds. Following the dosing period, the extentof proliferation was measured by adding 1/10 (vol/vol) AlamarBluereagent to every well and incubating the plates for a further 4 hours.The reaction was stopped by the addition of SDS to a final concentrationof 0.1%. Fluorescence was measured at 545 nm (excitation) and 600 nm(emission). GI50 values were determined for each test compound acrossthe panel.

The four cell lines were found to be sensitive to a TAK1 inhibitor. SeeFIG. 3. The correlation between the sensitivity to TAK1 shRNA and smallmolecule kinase inhibitor is striking, emphasizing the role of TAK1kinase activity in the survival of Lymphoma cells carrying the t(14;18).

Example 3 The following example was performed to determine inhibition ofcellgGrowth by a TAK1 inhibitor comprising a small molecule.

In order to demonstrate that the kinase function of TAK1 is critical forlymphoma cell survival, four small molecule inhibitors, i,e., compound 1is2-[(aminocarbonyl)amino]-5-[4-(morpholin-4-ylmethyl)phenyl]thiophene-3-carboxamide,compound 2 is2-[(aminocarbonyl)amino]-5-[4-(1-piperidin-1-ylethyl)phenyl]thiophene-3-carboxamide,compound 3 is3-[(aminocarbonyl)amino]-5-[4-(morpholin-4-ylmethyl)phenyl]thiophene-2-carboxamideand compound 4 is3-[(aminocarbonyl)amino]-5-(4-{[(2-methoxy-2-methylpropyl)amino]methyl}phenyl)thiophene-2-carboxamide,of TAK kinase were tested in a panel of leukaemia and lymphoma celllines, five of which (OCI-LY19, DOHH2, Karpas231, WSU-NHL and SUDHL4)carry the t(14;18) translocation. The TAK1 inhibitors are known in theart (see for example, WO 2003010158, WO 2003010163 and WO2004063186 thedisclosures of which are incorporated by reference herein). All celllines were plated at 10,000 cells/well in flat-bottomed 96 well platesand dosed with test compounds in triplicate over a 10 point dosing rangefrom 0 to 30 μmolesL⁻¹. All cell lines were incubated with testcompounds for a total of 72 hours. Background levels were determined fora control (undosed) plate within 2 hours of dosing test compounds.Following the dosing period, the extent of proliferation was measured byadding 1/10 (vol/vol) AlamarBlue reagent to every well and incubatingthe plates for a further 4 hours. The reaction was stopped by theaddition of SDS to a final concentration of 0.1%. Fluorescence wasmeasured at 545 nm (excitation) and 600 nm (emission). Growth inhibition50 (GI50) values were determined for each test compound across thepanel. See Table 4.

TAK1 Compound pIC50 OCI-LY19 DOHH2 Karpas231 WSU-NHL SUDHL4 Number(enzyme) DLBCL FL B-ALL B-NHL DLBCL 1 6.9 0.124 0.127 0.30 0.37 6.39 27.3 0.005 0.014 0.14 0.25 2.42 3 7 0.085 0.175 0.16 0.42 2.72 4 7.20.054 0.101 0.06 0.27 3.08 ARH77 HEL92.1.7 Raji Plasma Compound MEC1Erythro- KG1a Jurkat Burkitts cell Number B-CLL leukemia AML T-ALLLymphoma leukemia 1 1.34 0.73 0.45 15.86 15.22 1.17 2 0.16 0.17 0.404.39 3.5 0.25 3 0.63 0.50 0.43 >30 >30 0.48 4 2.99 1.47 1.09 10.09 >303.72

Table 4 shows GI50 values (μM) for 4 test compounds against a panel ofhuman haematological tumor cell lines.

The TAK1 inhibitor compounds were significantly more potent compared tothe mean in four out of five cell lines that carried the t(14;18)chromosomal translocation. This profile was differentiated from othercompounds that inhibit other pathways (data not shown). Table 5 showsthe GI50 values (μM) for a TAK1 kinase inhibitor against a panel ofmultiple myeloma tumour cell lines. The results indicate that a distinctset of myeloma cells are responsive to TAK1 inhibitors.

JJN-3 L-363 RPMI-8226 MOLP-8 ARH-77 KARPAS-620 Compd TAK1 plasma cellplasma cell AM0-1 Multiple Multiple IM-9 plasma cell plasma cell NumberpIC50 leukemia leukemia plasmacytoma myeloma myeloma B lymph leukemialeukemia 4 7.2 0.52 0.35 0.91 1.60 0.09 0.21 3.72 0.14

Table 5 shows GI50 values (μM) for compound 4 against a panel of humanmultiple myeloma cell lines

Table 6 shows the GI50 values (μM) for a TAK1 kinase inhibitor against apanel of human B-cell lymphoma cell lines. The experiments to generatethe results for both Tables 5 and 6 were performed as described above.The results indicate that a distinct set of human B-cell tumor cells areresponsive to TAK1 inhibitors.

NAMALWA Compd TAK1 SC-1 JEKO-1 Burkitts MEC-1 Number pIC50 FL MCLLymphoma B-CLL 4 7.2 2.88 0.29 2.96 2.99 WSU U937 Ramos Raji DERL 2DLCL2 Histiocytic Burkitts Burkitts Compd JVM-3 T cell B cell lymph-Lymph- Lymph- Number B-PLL lymphoma lymphoma oma oma oma 4 0.14 0.311.95 0.12 0.21 >30

Table 6 shows GI50 values (μM) for compound 4 against a panel of human Bcell lymphoma cell lines

Some of the TAK inhibitors used in the study belong to a large class ofthiophene carboxamide ureas that are known to inhibit other enzymes withsimilar potency against TAK1, such as FLT3, CHK1, ARK5 and Aurora Bkinase. Hence in order to rule out any off target effects of TAK1inhibitors in lymphoma and myeloma cell lines, we further utilized acommercially available TAK1 specific inhibitor, LL-Z-1640-2, which is a(3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione(Iris Biotech, GmbH; see WO-00248135). Table 7 shows the GI50 values(μM) for the TAK1 kinase inhibitor, LL-Z-1640-2 against a panel ofB-cell lymphoma cell lines.

WSU- OCI- DLCL MEC1 JVM-3 TAK1 SUDHL4 KARPAS231 LY19 B cell DOHH2 B- B-JEKO-1 Compd Number pIC50 DLBCL B-ALL DLBCL lymphoma FL CLL PLL MCLLL-Z-1640-2 6.8 1.64 0.95 0.23 0.02 0.39 0.73 0.71 0.07

Table 7 shows GI50 values (μM) for another TAK1 kinase inhibitor againsta panel of human B cell lymphoma cell lines

Table 8 shows the GI50 values (μM) for the TAK1 kinase inhibitor,LL-Z-1640-2 against a panel of multiple myeloma tumour cell lines. Theexperiments were performed as described above. The results indicatethat, similar to the thiophene carboxamide ureas a distinct set ofB-cell lymphoma and myeloma cells are responsive to TAK1 inhibitors.

JJN-3 L-363 TAK1 plasma cell plasma cell AM0-1 Compd pIC50 leukemialeukemia plasmacytoma LL-Z-1640-2 6.8 32.43 32.43 0.57 ARH-77 KARPAS-RPMI- MOLP-8 plasma 620 8226 Multiple IM-9 B cell plasma cell Compd M.Mmyeloma lymphoblastoid leukemia leukemia LL-Z- 1.41 10.44 0.02 1.24 ND1640-2

Table 8 shows GI50 values (μM) for another TAK1 kinase inhibitor againsta panel of human multiple myeloma cell lines

Example 4 Genomic Analysis of TAK1 Pathways in DLBCL 1. Tak1 PathwaysGenes

Genes in Tak1 pathways were assembled based on the public information.The genes that are involved in the signaling of ALK, FAS, MAP kinase,IL1 receptor, TGF-beta, TNF receptor, thrombin and protease-activatedreceptor, Toll-like receptor, WNT, and antigen receptor were included.The genes were mapped to Affymetrix probesets based on the annotationsavailable from Affymetrix(http://www.affymetrix.com/analysis/index.affx) (Table 1)

2. Gene Expression Data

The gene expression data of 176 newly diagnosed diffuse large B celllymphoma (DLBCL) patients were generated with Affymetrix U133A/B genechip and were made publicly available by Margaret Shipp's group at DanaFaber Cancer Institute ( ). The raw data were downloaded fromhttp://www.broad.mit.edu/cgi-bin/cancer/datasets.cgi, and furtherprocessed and analyzed as described below.

3. Data Preprocessing and Analysis 3.1 QC:

In order to verify data quality, and generate gene expression results,the raw data (.CEL files) of the DLBCL samples were loaded intoAffymetrix Expression Console 1.0 (Affymetrix Inc.) and analyzed usingMAS5 algorithm. The following criteria were used the filter out sampleswith low quality data: 1) scaling factor <4; 2) rawQ <5; 3) 3′/5′ ratiofor both actin and GAPDH <5; 4) percentage of present call >20 for chipA or >10 for chip B. As a result of the QC procedure, 113 samples (Table3) were kept for further analysis.

3.2 Normalization:

Array normalization: The parameters for MAS5 algorithm were set tonormalize each array using all probesets on the array, and the trimmedmean value for each array was preset to 100. Probeset normalization: Theexpression matrix generated by MAS5 were further normalized so that themean of each probeset was centered to zero.

3.3 Sample Clustering:

For unsupervised clustering analysis, the normalized expression matrixwas loaded into GeneSpring GX 7.3.1 (Agilent Inc.). A 2-way hierarchicalclustering was performed using only probeset IDs from table 2. Spearmancorrelation was used as the similarity measure in the clustering.

Results:

The 113 newly diagnosed DLBCL samples were separated into 3 distinctsubclasses based on their expression pattern of Tak1 genes. Theinformative genes (the genes that are differentially expressed among the3 patient subclass) were further divided into 7 groups (A-F) based ontheir distinct expression patterns. Most of the informative genes inGroup 2 are down-regulated compared to the other 2 groups, suggestingthe samples in this group represent a patient population that isinsensitive to Tak1-targeted therapy.

1. A method of inhibiting B cell tumour cell proliferation by contactinga B cell tumour cell with a TAK1 inhibitor.
 2. The method of claim 1wherein the B cell tumour is a non-Hodgkin's lymphoma, a Hodgkin'slymphoma, a chronic lymphocytic leukaemia, or a multiple myeloma.
 3. Amethod of treating a patient having a B cell tumour by administering aTAK1 inhibitor.
 4. The method of claim 3 wherein the B-cell tumour is anon-Hodgkin's lymphoma, a Hodgkin's lymphoma, a chronic lymphocyticleukaemia (CLL) or a multiple myeloma.
 5. The method of claims 2 or 4wherein the non-Hodgkin's lymphoma is a follicular lymphoma, a diffuselarge B cell lymphoma (DLBCL) of activated B cell (ABC) type, a diffuselarge B cell lymphoma (DLBCL) of germinal center B cell (GCB) type, amantle zone lymphoma (MZL), Mantle cell lymphoma (MCL), Primarymediastinal B-cell lymphoma (PMBCL) or MALT Lymphoma.
 6. The method ofclaim 5 wherein the non-Hodgkin's lymphoma has a t(14;18)(q32;q21)translocation, a t(11;18)(q21;q21) translocation, a t(1;14)(p22;q32), anamplification of chromosome 18, an amplification of chromosome 6, or anamplification, as defined by comparative genomic hybridization, ofspecific regions of BCL-10, CARD11, TRAF6 or TAK1.
 7. The method ofclaims 2 or 4 wherein the B-cell tumour is CLL.
 8. A method of treatinga patient having a deregulated TAK1 signalling transduction molecule byadministering a TAK1 inhibitor.
 9. The method of claim 8 wherein theTAK1 signalling transduction molecule is Malt1, BCL-10, BCL2, TAB1,TAB2, TAK1, TRAF2, TRAF6, TAK1, CARD11, IRAK1, IRAK4, API1, API2, API3,API4 or NFkappaB target genes.
 10. A method of inhibiting the growth ofa solid tumour by contacting the tumour with a TAK1 inhibitor.
 11. Themethod of claim 10, wherein the solid tumour is selected from the groupconsisting of a tumour of the head and neck, breast, ovary, lung,pancreas, colon, prostate, or skin.
 12. A method of treating a patienthaving a solid tumour by administering a TAK1 inhibitor.
 13. The methodof claims 10 or 12, wherein the solid tumour can be a tumour of the headand neck, breast, ovary, lung, pancreas, colon, prostate, liver, orskin.
 14. A method of selecting a patient having a tumour that issusceptible to treatment with a TAK1 inhibitor, comprising determiningif the patient has a genetic mutation of a t(14;18)(q32;q21)translocation, a t(11;18)(q21;q21) translocation, a t(1;14)(p22;q32)translocation, or an amplification of chromosome 18, whereby thepresence of a mutation indicates the tumour is susceptible to treatment.15. A method of selecting a patient having a tumour that is susceptibleto treatment with a TAK1 inhibitor, comprising determining if thepatient has a deregulated TAK1 signalling transduction molecule, whereinthe presence of the deregulated TAK1 signalling transduction molecule isan indication that the patient is susceptible to treatment with a TAK1inhibitor.
 16. A method of inhibiting proliferation of a T cell leukemiaand T-cell lymphomas by contacting a T cell leukaemia and T-celllymphoma with a TAK1 inhibitor.
 17. The method of claim 16, wherein theT cell leukemia is a T-cell acute lymphoblastic leukemia (T-ALL), orT-cell lymphomas, for example, peripheral T-cell lymphoma (PTCL), T-celllymphoblastic lymphoma (T-CLL), cutaneous T-cell lymphoma (CTCL) andadult T-cell lymphoma (ATCL).
 18. A method of selecting a mammal havingor suspected of having a tumour for treatment with a TAK1 inhibitordrug, the method comprising providing a biological sample from a subjecthaving cancer and testing the biological sample for expression of anyone of the genes listed in Table 1, or their gene products, thereby topredict an increased likelihood of response to the TAK1 inhibitor drug.